Haberlea darkness 2018 gene expression

The desiccation-tolerant plant Haberlea rhodopensis can withstand months of darkness without any visible senescence. Here, we investigated the molecular mechanisms of this adaptation to prolonged (30 d) darkness and subsequent return to light. H. rhodopensis plants remained green and viable throughout the dark treatment. Transcriptomic analysis revealed that darkness regulated several transcription factor (TF) genes. Stress- and autophagy-related TFs such as ERF8, HSFA2b, RD26, TGA1, and WRKY33 were up-regulated, while chloroplast- and flowering-related TFs such as ATH1, COL2, COL4, RL1, and PTAC7 were repressed. PHYTOCHROME INTERACTING FACTOR4, a negative regulator of photomorphogenesis and promoter of senes-cence, also was down-regulated. In response to darkness, most of the photosynthesis- and photorespiratory-related genes were strongly down-regulated, while genes related to autophagy were up-regulated. This occurred concomitant with the induction of SUCROSE NON-FERMENTING1-RELATED PROTEIN KINASES (SnRK1) signaling pathway genes, which regulate responses to stress-induced starvation and autophagy. Most of the genes associated with chlorophyll catabolism, which are induced by darkness in dark-senescing species, were either unregulated (PHEOPHORBIDE A OXYGENASE, PAO; RED CHLOROPHYLL CATABOLITE REDUCTASE, RCCR) or repressed (STAY GREEN-LIKE, PHEOPHYTINASE, and NON-YELLOW COLORING1). Metabolite profiling revealed increases in the levels of many amino acids in darkness, suggesting increased protein degrada-tion. In darkness, levels of the chloroplastic lipids digalactosyldiacylglycerol, monogalactosyldiacylglycerol, phosphatidylglyc-erol, and sulfoquinovosyldiacylglycerol decreased, while those of storage triacylglycerols increased, suggesting degradation of chloroplast membrane lipids and their conversion to triacylglycerols for use as energy and carbon sources. Collectively, these data show a coordinated response to darkness, including repression of photosynthetic, photorespiratory, flowering, and chloro-phyll catabolic genes, induction of autophagy and SnRK1 pathways, and metabolic reconfigurations that enable survival under prolonged darkness.耐脱水植物紫萼苣苔（Haberlea rhodopensis）可在数月黑暗环境中存活且无可见衰老症状。本研究针对该物种适应长期（30天）黑暗环境及后续复光的分子机制展开探究。实验期间，紫萼苣苔植株始终保持绿色且具备生活力。转录组分析显示，黑暗环境调控了多个转录因子（transcription factor, TF）基因的表达：与胁迫及细胞自噬相关的转录因子如ERF8、HSFA2b、RD26、TGA1及WRKY33均被上调，而与叶绿体及开花相关的转录因子如ATH1、COL2、COL4、RL1及PTAC7则被抑制。作为光形态建成负调控因子与衰老促进因子的光敏色素互作因子4（PHYTOCHROME INTERACTING FACTOR4），其表达同样被下调。在黑暗响应过程中，绝大多数光合作用与光呼吸相关基因的表达显著下调，而细胞自噬相关基因则被诱导上调。这一变化与蔗糖非发酵1相关蛋白激酶（SUCROSE NON-FERMENTING1-RELATED PROTEIN KINASES, SnRK1）信号通路基因的诱导同步发生，该通路负责调控胁迫诱导的饥饿响应及细胞自噬过程。对于黑暗诱导衰老的物种中由黑暗触发的叶绿素降解代谢相关基因，其中多数要么未被调控（如脱镁叶绿酸a氧化酶PHEOPHORBIDE A OXYGENASE, PAO、红色叶绿素代谢产物还原酶RED CHLOROPHYLL CATABOLITE REDUCTASE, RCCR），要么被抑制（如持绿类似蛋白STAY GREEN-LIKE、脱植基叶绿素酶PHEOPHYTINASE及非黄化着色1（NON-YELLOW COLORING1, NYC1））。代谢组分析结果显示，黑暗环境下植株体内多种氨基酸水平升高，提示蛋白质降解过程增强。黑暗环境中，叶绿体脂质成分包括双半乳糖基二酰甘油、单半乳糖基二酰甘油、磷脂酰甘油及硫代异鼠李糖基二酰甘油的含量下降，而储存型三酰甘油的含量则上升，表明叶绿体膜脂发生降解并转化为三酰甘油，以作为能量与碳源使用。综上，本研究数据表明紫萼苣苔对黑暗环境存在协同响应机制，包括抑制光合、光呼吸、开花及叶绿素降解相关基因的表达，诱导细胞自噬及SnRK1信号通路，同时发生代谢重编程，从而使其能够在长期黑暗环境中存活。